Where next for Star Trek: Discovery in season three? The clues are in the mystery shorts

When Star Trek Discovery debuted in 2017, marking the return of the classic science fiction series to episodic format after a 12-year cinematic sojourn, it proved contentious with fans. With perceived plot holes and characters that went unnamed onscreen for the entire first year, Discovery created more questions than it answered, even as it attempted to explore facets of Trek history that had previously only been mentioned.

The second season seemed in large part to be a course correction. The main story arc addressed the major continuity gaps the show had created, but by the time the credits rolled on the recent season finale, the groundwork had been laid for Discovery to become a very different show going forwards.

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Which leads us to question: where next for Star Trek's odd child? Needless to say, spoilers for Star Trek Discovery season two follow.

Ultimately, it seemed the second season of Discovery was when the showrunners finally realised what fans had been pointing out since day one: the show simply doesn't work as a prequel to the original Star Trek. With series lead Sonequa Martin-Green established as Spock's never-before-mentioned adoptive sister Michael Burnham, the Discovery ship housing advanced teleportation technology (its experimental Spore Drive, allowing instantaneous travel across the galaxy via the "mycelial network") that would have rendered the entirety of Star Trek Voyager moot, and supporting or background characters displaying technological augments that outpaced those used in shows set hundreds of years later, too much of Discovery just didn't fit.

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As such, a lot of the second season was spent addressing those self-created problems. A literal roll call as Anson Mount's Captain Christopher Pike took command served to identify at least the Discovery's bridge crew for viewers, while other characters were killed off to seemingly hand-wave away the anachronistic bio-tech problem. By the end of the finale, the ship and its crew were catapulted nearly a thousand years into the future, departing through a temporal wormhole created by Burnham. The in-show reason was to prevent a malevolent AI, Control, from gaining a celestial data cache in Discovery's memory banks that would enable it to wipe out all life in the galaxy, but in practical terms it removes the problems Discovery creates for the Trek canon entirely.

Although the episode itself gives no clue as to what awaits the Discovery after its time jump – the remainder of the episode following its disappearance is given over to a rather heavy-handed explanation for why no-one has ever mentioned the ship or its crew – there are hints laid elsewhere that may indicate what's to come for the show when it returns for its third season.

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The main clue may be found in the Star Trek: Short Treks episode ‘Calypso’. There's a reasonable chance you may have missed this – the four short episodes were exclusive to CBS All Access (where Star Trek Discovery streams in the US) for a while, and when they finally arrived on Netflix UK, they ended up buried under the 'Trailers and More' section of Discovery's listing.

The shorts, however, weren't just frivolous bonus episodes – two have already proved relevant to Discovery season two. ‘Runaway’ introduced Me Hani Ika Hali Ka Po, the genius teenage queen of a world essential in facilitating Discovery's time-jump, while ‘The Brightest Star’ revealed how Saru became the first and only Kelpien to join Starfleet, and set up a major change for his species that played out in the main show. Although the fourth short, ‘The Escape Artist’ was a forgettable and unimportant look at the ever-annoying Harry Mudd, ‘Calypso’ was loaded with promise.

First is its setting: ‘Calypso’ takes place in the 33rd century, which roughly matches Discovery's target destination. The episode, written by Pulitzer-winning author Michael Chabon, sees a human soldier called Craft (Aldis Hodge) rescued by Zora, the seemingly sentient AI that maintains Discovery. The ship is abandoned, with Zora ordered to "maintain position" by an unnamed Captain whom Craft thinks "has been dead for a thousand years".

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Time can get weird in Star Trek, so there's no reason to think that because Zora has been alone for a millennium, the crew are actually gone-gone. The experimental method of time travel could result in something like a temporal asynchronicity, where the crew hasn't 'caught up' with the ship itself – and when they do, they could be met with a vessel that has been waiting for them.

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It's also worth considering that when Discovery left for the future, the inert shell of Control was onboard. The Zora AI says she was waiting "almost a thousand years – I spent most of it evolving myself", which could indicate some reappropriation of Control's code, in a more benign fashion.

Perhaps more interesting, though, is what ‘Calypso’ tells us about the state of the universe Discovery will be exploring when the show returns. Craft was at war with a force called the V'Draysh, which Chabon confirmed is a syncope – or corruption – of "Federation". Craft's world, Alcor IV, isn't in Discovery's data banks, indicating it wasn't colonised until after the ship jumped forwards in time, and its seeming independence from the remnants of the Federation shows the once-noble organisation has become something terrible.

We don't see any V'Draysh ships, beyond the stolen escape pod that Zora finds Craft in, but the short episode gives a lot away about their society. The V'Draysh are obsessed with culture from "The Long Ago", an era which includes at least 20th century media. Even Craft's escape pod is equipped with a media library of 542,000 files, which play on loop in a sort of indoctrination fashion. The films and videos included are all Earth media too, perhaps indicating the Federation descended into an exclusionary mono-culture over the centuries.

If so, it could provide fertile ground for Discovery to explore when it returns, from our own contemporary society's obsession with nostalgia and reboots – of which Discovery itself is guilty – to more blatant political metaphors. Trek is always best when it has real-world scenarios to bounce off, and contrasting, for instance, Trump's proposed border wall with the V'Draysh's 'Earth first' outlook could be fascinating.

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Moving Discovery to the far future also opens up some scintillating narrative possibilities, ones that could tie into some of Star Trek creator Gene Roddenberry's own ideas. Discovery's millennial jump will place it farther along in the franchise's timeline than we've ever seen before, allowing for truly new voyages and encounters and letting the show return in part to its exploratory roots. But if the V'Draysh are a broken, fallen Federation, the new period also potentially presents a lone Starfleet vessel without backup, command structure, or even any recognisable home, left to fend for itself and try to uphold its own set of ethics when the universe has changed around it.

If that sounds familiar, it's because it overlaps with the setup of the aforementioned Star Trek Voyager – jettisoned in space, if not time – but also the 2000 sci-fi show Andromeda. Loosely inspired by a Roddenberry idea, it saw a lone ship from a Systems Commonwealth frozen in time for centuries, emerging after that organisation had fallen, and fighting to restore civilisation in a war-torn and corrupt era.

While Andromeda was a low-budget, unambiguous mirror to Star Trek, that loose Roddenberry idea at the heart of it is captivating. Seeing it done properly, with Discovery's budget, could result in some of the most compelling material Star Trek has had in years. What does the Federation mean, when the Federation itself is no more? Can the bright union of worlds be restored, or will the V'Draysh's insular obsession with past glories be its final legacy? Essentially, is there a place for hope at the end of the universe?

Discovery's finale and ‘Calypso’'s setting suggest a fascinating set of questions, ones that could reaffirm or deconstruct what Star Trek means. If the third season pans out as it seems the showrunners have set it up to, they are questions the show is well-positioned to explore when it returns.